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Functions, Transmission and Emission of the Canopy Microbiota Tania Fort

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Functions, Transmission and Emission of the Canopy Microbiota Tania Fort Functions, transmission and emission of the canopy microbiota Tania Fort To cite this version: Tania Fort. Functions, transmission and emission of the canopy microbiota. Vegetal Biology. Univer- sité de Bordeaux, 2019. English. NNT : 2019BORD0338. tel-02869590 HAL Id: tel-02869590 https://tel.archives-ouvertes.fr/tel-02869590 Submitted on 16 Jun 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE PRESENTÉE POUR OBTENIR LE GRADE DE DOCTEUR DE L’UNIVERSITE DE BORDEAUX ECOLE DOCTORALE SCIENCES ET ENVIRONNEMENTS ECOLOGIE ÉVOLUTIVE, FONCTIONNELLE, ET DES COMMUNAUTÉS Par Tania Fort Fonctions, transmission et émission du microbiote de la canopée Sous la direction de Corinne Vacher Soutenue le 10 décembre 2019 Membres du jury : Mme. Anne-Marie DELORT Directrice de recherche Institut de Chimie de Clermont-Ferrand Rapporteuse M. Stéphane Uroz Directeur de recherche INRA Nancy Rapporteur Mme. Patricia Luis Maître de conférence Université de Lyon 1 Rapporteuse Mme. Annabel Porté Directrice de recherche INRA Bordeaux Présidente Mme. Corinne Vacher Directrice de recherche INRA Bordeaux Directrice Fonctions, transmission et émission du microbiote de la canopée. Les arbres interagissent avec des communautés microbiennes diversifiées qui influencent leur fitness et le fonctionnement des écosystèmes terrestres. Contrairement aux micro-organismes associés aux racines et au sol, les micro-organismes qui colonisent la canopée forestière sont encore mal connus. L’objectif de cette thèse est de mieux comprendre les fonctions des micro-organismes associés aux parties aériennes des arbres (feuilles, tiges, graines) ainsi que leur dynamique de transmission verticale (de l’arbre à ses descendants) et horizontale (émission de l’arbre vers l’atmosphère), en combinant des analyses d’écologie moléculaire et d’écophysiologie végétale. Le chapitre II montre que les communautés fongiques de la phyllosphère du hêtre (Fagus Sylvatica) sont fortement structurées par l’arbre hôte, contrairement aux bactéries qui sont plus fortement influencées par les gradients environnementaux verticaux à l’intérieur de la canopée. Dans les deux cas, les variations de composition microbienne sont mieux expliquées par la chimie foliaire que par la morphologie ou physiologie. Ce chapitre révèle aussi la prédominance des champignons pathogènes dans la phyllosphère du hêtre, ainsi qu’une forte abondance de saprotrophes en bas de la canopée. La phyllosphère du hêtre contenait très peu de bactéries diazotrophes, contrairement à d’autres espèces d’arbres. Le chapitre III met en évidence la présence de champignons dans les tissus internes des glands du chêne sessile (Quercus petraea), y compris l’embryon, suggérant que le microbiote peut être transmis verticalement de l’arbre mère à ses descendants et influencer la régénération forestière. Les glands contiennent en particulier plusieurs espèces de champignons pathogènes, en association avec leurs mycoparasites. Ces communautés fongiques varient significativement en fonction de l’arbre mère et de la population de chêne. Enfin, le chapitre IV teste un prototype de mesure des flux d’émissions bactériennes au-dessus des couverts végétaux. Il montre que la moitié des espèces capturées dans l’atmosphère est présente sur la surface des feuilles et sugg ère que la composition des bioaérosols est fortement influencée par la plante cultivée dominante en Nouvelle- Aquitaine, la vigne (Vitis vinifera). Cette thèse apporte donc des éléments pour modéliser la dynamique et l’évolution du système arbre-microbiote-atmosphère, qu’il conviendra de renforcer et d’intégrer aux connaissances sur le sol afin de répondre aux défis posés par le changement climatique. Functions, transmission and emission of the canopy microbiota. Trees interact with diverse microbial communities that influence their fitness and the functioning of terrestrial ecosystems. Unlike microorganisms associated with roots and soil, microorganisms that colonize the forest canopy are still poorly understood. The objective of this thesis is to better understand the functions of microorganisms associated with the aerial parts of trees (leaves, stems, seeds) as well as their vertical (from the tree to its descendants) and horizontal (emission from the tree to the atmosphere) transmission dynamics, by combining molecular ecology and plant ecophysiology analyses. The chapter II shows that fungal communities in the beech phyllosphere (Fagus Sylvatica) are strongly structured by the host tree, unlike bacteria, which are more strongly influenced by the vertical environmental gradients within the canopy. In both cases, variations in microbial composition are better explained by foliar chemistry than by morphology or physiology. This chapter also reveals the predominance of pathogenic fungi in the beech phyllosphere, as well as a high abundance of saprotrophic fungi at the bottom of the canopy. The beech phyllosphere contained very few diazotrophic bacteria, unlike other tree species. The chapter III highlights the presence of fungi in the internal tissues of acorns of sessile oak (Quercus petraea), including the embryo, suggesting that the mycobiota can be transmitted vertically from the mother tree to its descendants and influence forest regeneration. Acorns contain several species of pathogenic fungi, in association with their mycoparasites. These fungal communities differ significantly among mother trees and oak populations. Finally, the chapter IV tests a prototype for measuring bacterial emission fluxes over plant canopies. It shows that half of the species captured in the atmosphere are present on leaf surfaces and suggests that the composition of bioaerosols is strongly influenced by the dominant cultivated plant in New Aquitaine, the vine (Vitis vinifera). This thesis therefore provides elements for modelling the dynamics and evolution of the tree- microbiota-atmosphere system, which will need to be strengthened and integrated into knowledge about soil in order to meet the challenges posed by climate change. Unité de recherche UMR 1202 Biodiversité, Gènes et Communautés (BIOGECO), INRA, 33610, Pessac, France 1 Remerciements Afin de présenter convenablement ce manuscrit, il convient, tout d’abord, de “rendre à César ce qui appartient à César”. Je ne saurais donc exposer le travail de ces trois dernières années sans souligner la pléiade de personnes qui ont contribué à sa réalisation. Tout d’abord, je tiens à remercier l’Université de Bordeaux et le LabEx COTE qui ont tous les deux financé ma thèse, les projets réalisés lors de celle-ci et mes déplacements à l’étranger. Je tiens à remercier ma directrice de thèse, Corinne Vacher, pour m’avoir conseillée sur les analyses statistiques, la manière de présenter mon travail à l’oral comme à l’écrit. Les longues heures passées à valoriser mes idées, ton soutien et tes encouragements lors de “cas de force majeure” m’ont permis de garder le cap lorsque la fatigue et le stress l’emportait. Je salue également ton entrain et ta confiance pour m’avoir proposée de nombreux projets, malheureusement la magie de la biologie moléculaire en aura décidé autrement. Je remercie également Lisa Wingate, Amy Zanne, Heidy Schimann, Arndt Hampe, et Nicolas Fanin pour m’avoir conseillé toute au long de ma thèse, vos nombreuses idées, toujours plus créatives les unes que les autres, m’ont permis de voir au-delà de mes thématiques de thèse et de tisser des liens avec un communauté de scientifique plus étendue. Amy, I’ld also like to thank you and your team, Amy Milo, Marissa Lee, for your welcome in Washington DC. I had a wondeful time in your lab and this is definitely one the best experience I had during my thesis! Merci à Heidy Schimann, Elianne Louisanna et Marc Buée pour m’avoir fait vivre l’authentique expérience guyanaise. Ces quelques semaines passées au cours de la forêt tropicale demeurent une des expériences les plus enrichissantes que j’ai vécues. Un grand merci à Yves Brunet, pour voir passer ces dernières nuits à travailler sur le dernier chapitre de ma thèse. Je remercie chaleureusement et très sincèrement toutes les petites mains qui m’ont aidé à venir à bouts des milliers d’échantillons triés et traités lors de ma thèse. Je pense notamment aux personnes sur place lors des campagnes d’échantillonnage: Charlie Pauvert, Thomas Caignard, Jean-Marc Louvet, Corinne Vacher, Lisa Wingate, Adria Barbeta, Régis Burlett, Raphaël Segura, Yannick Mellerin, Nicolas Cheval, Bernard Dokhelar, Jean luc Denou, Luc Puzos, Xavier Capdevielle, Yves Brunet, Frédéric Delmas, Jean-Marc Bonnefond, Didier Garrigou. Un merci tout particulier aux personnes qui ont passé des semaines voir des mois avec (ou sans) moi dans les labos. Je pense notamment à Emilie Chancerel, Patricia Balias, Eliane Louisanna, Julie Faivre d’Arcier, Céline 2 Lalanne, Martine Martin, Marie Massot, Patrick Leger, Yves Gibbon, Dinia Carty, Amandyne Linares- Maurizi. Ma plus grande reconnaissance va à tous les thésards qui m’ont supporté et aidé lors de ces trois dernières années et qui sont maintenant devenus
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